From db43ba615c9084963f743df86512bd92ac88c8af Mon Sep 17 00:00:00 2001
From: Johannes Ranke <johannes.ranke@jrwb.de>
Date: Sun, 28 Jul 2024 18:56:54 +0200
Subject: Move coverage report from travis to github actions

---
 .Rbuildignore                        |  2 ++
 .github/.gitignore                   |  1 +
 .github/workflows/test-coverage.yaml | 61 ++++++++++++++++++++++++++++++++++++
 .travis.yml                          |  3 --
 README.md                            |  5 ++-
 codecov.yml                          | 14 +++++++++
 6 files changed, 82 insertions(+), 4 deletions(-)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index e7cbe786..1a243475 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -35,3 +35,5 @@
 ^vignettes/web_only/.*$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^codecov\.yml$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 00000000..2d19fc76
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 00000000..fefc52e2
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.travis.yml b/.travis.yml
index 61b56979..006ba521 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,6 +24,3 @@ script:
 
 after_failure:
   - ./run.sh dump_logs
-
-after_success:
-  - travis_wait 40 ./run.sh coverage
diff --git a/README.md b/README.md
index 98e3d0a7..dee59ed9 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,12 @@
 # mkin
 
+<!-- badges: start -->
 [![](https://www.r-pkg.org/badges/version/mkin)](https://cran.r-project.org/package=mkin)
 [![mkin status badge](https://jranke.r-universe.dev/badges/mkin)](https://jranke.r-universe.dev/ui/#package:mkin)
 [![Build Status](https://app.travis-ci.com/jranke/mkin.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main)](https://app.travis-ci.com/jranke/mkin)
-[![codecov](https://codecov.io/github/jranke/mkin/branch/main/graphs/badge.svg)](https://app.codecov.io/gh/jranke/mkin)
+[![Codecov test coverage](https://codecov.io/gh/jranke/mkin/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jranke/mkin?branch=main)
+<!-- badges: end -->
+
 
 The [R](https://www.r-project.org) package **mkin** provides calculation routines for the analysis of
 chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 00000000..04c55859
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
-- 
cgit v1.2.1